[English] 日本語
Yorodumi
- EMDB-2370: The Respiratory Syncytial Virus nucleoprotein-RNA complex forms a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2370
TitleThe Respiratory Syncytial Virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid.
Map dataSubtomogram average of purified recombinant measles virus nucleocapsid
Sample
  • Sample: Purified recombinant measles virus nucleocapsids.
  • Virus: Measles virus
KeywordsRespiratory Syncytial Virus / nucleocapsid / cryo-electron tomography / sub-tomogram averaging
Biological speciesMeasles virus
Methodsubtomogram averaging / negative staining
AuthorsBakker SE / Duquerroy S / Galloux M / Loney C / Conner E / Eleouet JF / Rey FA / Bhella D
CitationJournal: J Gen Virol / Year: 2013
Title: The respiratory syncytial virus nucleoprotein-RNA complex forms a left-handed helical nucleocapsid.
Authors: Saskia E Bakker / Stéphane Duquerroy / Marie Galloux / Colin Loney / Edward Conner / Jean-François Eléouët / Félix A Rey / David Bhella /
Abstract: Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical ...Respiratory syncytial virus (RSV) is an important human pathogen. Its nucleocapsid (NC), which comprises the negative sense RNA viral genome coated by the viral nucleoprotein N, is a critical assembly that serves as template for both mRNA synthesis and genome replication. We have previously described the X-ray structure of an NC-like structure: a decameric ring formed of N-RNA that mimics one turn of the helical NC. In the absence of experimental data we had hypothesized that the NC helix would be right-handed, as the N-N contacts in the ring appeared to more easily adapt to that conformation. We now unambiguously show that the RSV NC is a left-handed helix. We further show that the contacts in the ring can be distorted to maintain key N-N-protein interactions in a left-handed helix, and discuss the implications of the resulting atomic model of the helical NC for viral replication and transcription.
History
DepositionApr 25, 2013-
Header (metadata) releaseMay 8, 2013-
Map releaseMay 29, 2013-
UpdateJul 24, 2013-
Current statusJul 24, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2370.png

Downloads & links

-
Map

FileDownload / File: emd_2370.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of purified recombinant measles virus nucleocapsid
Voxel sizeX=Y=Z: 6.5 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-3.70706797 - 1.41578865
Average (Standard dev.)-0.04789204 (±0.56955951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.56.56.5
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-3.7071.416-0.048

-
Supplemental data

-
Sample components

-
Entire : Purified recombinant measles virus nucleocapsids.

EntireName: Purified recombinant measles virus nucleocapsids.
Components
  • Sample: Purified recombinant measles virus nucleocapsids.
  • Virus: Measles virus

-
Supramolecule #1000: Purified recombinant measles virus nucleocapsids.

SupramoleculeName: Purified recombinant measles virus nucleocapsids. / type: sample / ID: 1000 / Oligomeric state: variable helices / Number unique components: 1

-
Supramolecule #1: Measles virus

SupramoleculeName: Measles virus / type: virus / ID: 1 / Name.synonym: MeV / Details: Purified recombinant nucleocapsid / NCBI-ID: 11234 / Sci species name: Measles virus / Virus type: OTHER / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No / Syn species name: MeV
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf21 / Recombinant plasmid: Rbac69

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsubtomogram averaging
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4 / Details: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 10 mM EDTA
StainingType: NEGATIVE
Details: Protein preparations were mixed with 10 nm colloidal gold and loaded onto freshly glow-discharged perforated C-flat carbon films (CF-22-2C, Protochips Inc.). Grids were then washed in 0.1% ...Details: Protein preparations were mixed with 10 nm colloidal gold and loaded onto freshly glow-discharged perforated C-flat carbon films (CF-22-2C, Protochips Inc.). Grids were then washed in 0.1% trehalose, and stained using 5% ammonium molybdate (pH 7.4) and 0.1% trehalose, drained and allowed to dry in air
GridDetails: Glow-discharged perforated C-flat carbon films (CF-22-2C, Protochips Inc.)
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeJEOL 2200FSC
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 40000
Specialist opticsEnergy filter - Name: Jeol / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
TemperatureMin: 97 K / Max: 293 K
Alignment procedureLegacy - Astigmatism: Corrected at 100k times mag in digital micrograph
DetailsRoom temperature stained grids imaged at LN2 temperatures.
DateJul 15, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 7 / Average electron dose: 131 e/Å2

-
Image processing

Final 3D classificationNumber classes: 1
Final reconstructionAlgorithm: OTHER / Software - Name: Etomo, Dynamo / Details: Subtomograms were picked from nine tomograms. / Number subtomograms used: 911
DetailsSubtomograms were manually picked. A starting model was obtained by manually aligning 100 subtomograms, all subtomograms were aligned to this starting model. To mitigate missing wedge artefacts, the orientations around the helical axis were randomised before further alignment.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more